Multiplex Pyrosequencing of Two Polymorphisms in DNA Repair Gene XRCC1

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Multiplex Pyrosequencing of Two Polymorphisms in DNA Repair Gene XRCC1 Tahar van der Straaten, Dinemarie Kweekel, Marco Tiller, Judith Bogaartz, Henk-Jan Guchelaar The Journal of Molecular Diagnostics Volume 8, Issue 4, Pages 444-448 (September 2006) DOI: 10.2353/jmoldx.2006.060018 Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Histograms of XRCC1 duplex pyrosequence assay as predicted by pyrosequence software. G399A (rs25487) is shown as blue bars and A576delA (rs2307177) is shown as red bars. The depicted genotypes are G399G and A576A (A), G399A and A576A (B), A399A and A576A (C), G399A and A576delA (D). The yellow areas indicate the nucleotides of interest (SNP). The Journal of Molecular Diagnostics 2006 8, 444-448DOI: (10.2353/jmoldx.2006.060018) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Representative pyrogram of XRCC1 duplex pyrosequence. A: The upper pyrogram shows G399G and A576A, middle pyrogram shows G399A and A576A, and the lower pyrogram shows A399A and A576A. Note that C399T is sequenced with antisense primer, and therefore the complementary nucleotides are shown. B: Pyrogram of A576C (and G399A) genotype that, due to the dispensation order, is genotyped as A576delA. The shaded nucleotides indicate the SNP of interest. The Journal of Molecular Diagnostics 2006 8, 444-448DOI: (10.2353/jmoldx.2006.060018) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Electropherogram of conventional sequence analysis of the observed genotypes. PCR product of a patient heterozygous for XRCC1 A576C was subcloned in pGEM-Teasy (Promega, Leiden, The Netherlands); several clones were taken for sequence analysis. The arrows indicate the nucleotide at codon-position 576 in the XRCC1 gene, upper graph 576C and lower graph 576A. The Journal of Molecular Diagnostics 2006 8, 444-448DOI: (10.2353/jmoldx.2006.060018) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Pyrogram of XRCC1 duplex pyrosequence with adapted sequence to analyze to detect A/C substitution at position 576. The C-nucleotide is dipensated after the A-nucleotide, allowing discrimination between A576A, A576delA, delA576delA, A576C, or C576C. The shaded nucleotides indicate the SNP of interest. The Journal of Molecular Diagnostics 2006 8, 444-448DOI: (10.2353/jmoldx.2006.060018) Copyright © 2006 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions